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#1 2014-07-06 15:02:25

CaptainKirk
Member
Registered: 2009-06-07
Posts: 391

My extra.db File is Haywire

Seems to me that I can't upgrade properly because of an ownership problem on extra.db but see here for yourself what I (no big expert in these things) have tried to do:

[kirk@arch ~]$ sudo pacman -Suy
[sudo] password for kirk: 
:: Synchronizing package databases...
 core                                                     110.7 KiB  1909K/s 00:00 [###############################################] 100%
 extra                                                   1742.9 KiB  2.71M/s 00:01 [###############################################] 100%
error: could not rename /var/lib/pacman/sync/extra.db.part to /var/lib/pacman/sync/extra.db (Operation not permitted)
 extra                                                   1742.9 KiB  1204K/s 00:01 [###############################################] 100%
error: could not rename /var/lib/pacman/sync/extra.db.part to /var/lib/pacman/sync/extra.db (Operation not permitted)
 extra                                                   1742.9 KiB  1256K/s 00:01 [###############################################] 100%
error: could not rename /var/lib/pacman/sync/extra.db.part to /var/lib/pacman/sync/extra.db (Operation not permitted)
error: failed to update extra (unexpected error)
 community                                                  2.2 MiB  2.51M/s 00:01 [###############################################] 100%
 archlinuxfr                                               19.2 KiB   176K/s 00:00 [###############################################] 100%
:: Starting full system upgrade...
error: could not open file /var/lib/pacman/sync/extra.db: No such device or address
error: could not open file /var/lib/pacman/sync/extra.db: No such device or address
error: could not open file /var/lib/pacman/sync/extra.db: No such device or address
error: could not open file /var/lib/pacman/sync/extra.db: No such device or address
error: could not open file /var/lib/pacman/sync/extra.db: No such device or address
error: could not open file /var/lib/pacman/sync/extra.db: No such device or address
error: could not open file /var/lib/pacman/sync/extra.db: No such device or address
resolving dependencies...
error: could not open file /var/lib/pacman/local/ldb-1.1.16-1/desc: No such file or directory
error: could not open file /var/lib/pacman/local/libgxps-0.2.2-3/desc: No such file or directory
looking for inter-conflicts...
error: failed to prepare transaction (could not satisfy dependencies)
:: nvidia: requires linux<3.15
[kirk@arch ~]$ sudo pacman -Suy IgnorePkg=nvidia
:: Synchronizing package databases...
 core is up to date
 extra                                                   1742.9 KiB  1746K/s 00:01 [###############################################] 100%
error: could not rename /var/lib/pacman/sync/extra.db.part to /var/lib/pacman/sync/extra.db (Operation not permitted)
 extra                                                   1742.9 KiB  1149K/s 00:02 [###############################################] 100%
error: could not rename /var/lib/pacman/sync/extra.db.part to /var/lib/pacman/sync/extra.db (Operation not permitted)
 extra                                                   1742.9 KiB   254K/s 00:07 [###############################################] 100%
error: could not rename /var/lib/pacman/sync/extra.db.part to /var/lib/pacman/sync/extra.db (Operation not permitted)
error: failed to update extra (unexpected error)
 community is up to date
 archlinuxfr is up to date
error: could not open file /var/lib/pacman/sync/extra.db: No such device or address
error: could not open file /var/lib/pacman/sync/extra.db: No such device or address
error: could not open file /var/lib/pacman/sync/extra.db: No such device or address
error: target not found: IgnorePkg=nvidia
[kirk@arch ~]$ df -H
Filesystem      Size  Used Avail Use% Mounted on
/dev/sda2        20G   16G  2.9G  85% /
dev             2.0G     0  2.0G   0% /dev
run             2.1G  795k  2.1G   1% /run
tmpfs           2.1G  443k  2.1G   1% /dev/shm
tmpfs           2.1G     0  2.1G   0% /sys/fs/cgroup
tmpfs           2.1G  869k  2.1G   1% /tmp
/dev/sda1       279M   37M  224M  14% /boot
/dev/sda4       374G  255G  101G  72% /home
/dev/sda3        99G   25G   70G  26% /srv
tmpfs           401M   17k  401M   1% /run/user/1000
[kirk@arch ~]$ lsblk
NAME   MAJ:MIN RM   SIZE RO TYPE MOUNTPOINT
sda      8:0    0 465.8G  0 disk 
├─sda1   8:1    0 282.4M  0 part /boot
├─sda2   8:2    0  18.6G  0 part /
├─sda3   8:3    0  93.1G  0 part /srv
└─sda4   8:4    0 353.7G  0 part /home
sdb      8:16   0 931.5G  0 disk 
├─sdb1   8:17   0 282.4M  0 part 
├─sdb2   8:18   0  18.6G  0 part 
├─sdb3   8:19   0 205.2G  0 part 
├─sdb4   8:20   0     1K  0 part 
└─sdb5   8:21   0 210.9G  0 part 
[kirk@arch ~]$ sudo ls /var/lib/pacman/sync -al
total 138152619027433
drwxr-xr-x     2 root  root     4096 Jul  6 17:45 .
drwxr-xr-x     4 root  root     4096 Jul  6 17:45 ..
-rw-r--r--     1 root  root    19638 Jul  6 17:08 archlinuxfr.db
-rw-r--r--     1 root  root  2358021 Jul  6 15:51 community.db
-rw-r--r--     1 root  root   113405 Jul  5 21:22 core.db
crwxr-x--T 21392 47825 17389    0, 0 Jan  1  1970 extra.db
-rw-r--r--     1 root  root   106743 Apr  6  2013 multilib.db
[kirk@arch ~]$ sudo chown root:root  /var/lib/pacman/sync/extra.db
chown: changing ownership of ‘/var/lib/pacman/sync/extra.db’: Operation not permitted
[kirk@arch ~]$ sudo rm  /var/lib/pacman/sync/extra.db
rm: cannot remove ‘/var/lib/pacman/sync/extra.db’: Operation not permitted
[kirk@arch ~]$ sudo ls /var/lib/pacman  -l
total 60
drwxr-xr-x 1055 root root 53248 Jun 18 14:45 local
drwxr-xr-x    2 root root  4096 Jul  6 17:45 sync

I can't chown it nor can I rm it. This is my personal desktop machine.Seems a gremlin has taken over my extra.db file. smile

Actually it's not a file because the first letter in ls -l is c. I don't even know what that means, even after Googling....

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#2 2014-07-06 15:27:16

karol
Archivist
Registered: 2009-05-06
Posts: 25,440

Re: My extra.db File is Haywire

c means https://en.wikipedia.org/wiki/Device_file
What's the output of

stat /var/lib/pacman/sync/extra.db
ls -l /var/lib/pacman/sync/extra.db

Last edited by karol (2014-07-06 15:29:20)

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#3 2014-07-06 15:29:44

CaptainKirk
Member
Registered: 2009-06-07
Posts: 391

Re: My extra.db File is Haywire

Thanks for the clarification. Here is the output:

$ sudo stat /var/lib/pacman/sync/extra.db
  File: ‘/var/lib/pacman/sync/extra.db’
  Size: 32701     	Blocks: 276305238049761 IO Block: 4096   character special file
Device: 802h/2050d	Inode: 275597      Links: 21392 Device type: 0,0
Access: (1750/crwxr-x--T)  Uid: (47825/ UNKNOWN)   Gid: (17389/ UNKNOWN)
Access: 1933-04-16 05:53:36.000000000 +0200
Modify: 1970-01-01 11:13:08.000000000 +0200
Change: 1970-01-01 11:05:01.000000000 +0200
 Birth: -

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#4 2014-07-06 16:16:50

falconindy
Developer
From: New York, USA
Registered: 2009-10-22
Posts: 4,111
Website

Re: My extra.db File is Haywire

chattr -i extra.db

blog | ±github

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#5 2014-07-06 16:27:08

CaptainKirk
Member
Registered: 2009-06-07
Posts: 391

Re: My extra.db File is Haywire

$ sudo chattr -i /var/lib/pacman/sync/extra.db
chattr: Operation not supported while reading flags on /var/lib/pacman/sync/extra.db

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#6 2014-07-06 16:53:28

karol
Archivist
Registered: 2009-05-06
Posts: 25,440

Re: My extra.db File is Haywire

What's going on with the timesatmps on that file? Uid and Gid don't look good either.
The file has the sticky bit set on (the last letter in the file permissions is 'T'). Try removing it with 'chmod -t'. (Nah, that shouldn't change anything).

Last edited by karol (2014-07-06 16:59:05)

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#7 2014-07-06 18:54:17

falconindy
Developer
From: New York, USA
Registered: 2009-10-22
Posts: 4,111
Website

Re: My extra.db File is Haywire

Actually, the "character special file" portion of the stat looks the most alarming. There's not enough context here. What filesystem is this? What have you done recently to the system?

blog | ±github

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#8 2014-07-06 20:36:01

CaptainKirk
Member
Registered: 2009-06-07
Posts: 391

Re: My extra.db File is Haywire

Filesystem? See below.

What did I do? Nothing, just ran pacman upgrades like a good boy. One day (a few weeks ago maybe) this problem came up. I was hoping it would just go away, but it hasn't. sad

Here are some fun commands I ran now:

[kirk@arch ~]$ sudo mount
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
sys on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)
dev on /dev type devtmpfs (rw,nosuid,relatime,size=1952992k,nr_inodes=488248,mode=755)
run on /run type tmpfs (rw,nosuid,nodev,relatime,mode=755)
/dev/sda2 on / type ext4 (rw,relatime,data=ordered)
securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)
tmpfs on /sys/fs/cgroup type tmpfs (ro,nosuid,nodev,noexec,mode=755)
cgroup on /sys/fs/cgroup/systemd type cgroup (rw,nosuid,nodev,noexec,relatime,xattr,release_agent=/usr/lib/systemd/systemd-cgroups-agent,name=systemd)
pstore on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime)
cgroup on /sys/fs/cgroup/cpuset type cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)
cgroup on /sys/fs/cgroup/cpu,cpuacct type cgroup (rw,nosuid,nodev,noexec,relatime,cpu,cpuacct)
cgroup on /sys/fs/cgroup/memory type cgroup (rw,nosuid,nodev,noexec,relatime,memory)
cgroup on /sys/fs/cgroup/devices type cgroup (rw,nosuid,nodev,noexec,relatime,devices)
cgroup on /sys/fs/cgroup/freezer type cgroup (rw,nosuid,nodev,noexec,relatime,freezer)
cgroup on /sys/fs/cgroup/net_cls type cgroup (rw,nosuid,nodev,noexec,relatime,net_cls)
cgroup on /sys/fs/cgroup/blkio type cgroup (rw,nosuid,nodev,noexec,relatime,blkio)
systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=22,pgrp=1,timeout=300,minproto=5,maxproto=5,direct)
hugetlbfs on /dev/hugepages type hugetlbfs (rw,relatime)
debugfs on /sys/kernel/debug type debugfs (rw,relatime)
mqueue on /dev/mqueue type mqueue (rw,relatime)
tmpfs on /tmp type tmpfs (rw)
configfs on /sys/kernel/config type configfs (rw,relatime)
binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,relatime)
/dev/sda1 on /boot type ext4 (rw,relatime,data=ordered)
/dev/sda4 on /home type ext4 (rw,relatime,data=ordered)
/dev/sda3 on /srv type ext4 (rw,relatime,data=ordered)
tmpfs on /run/user/1000 type tmpfs (rw,nosuid,nodev,relatime,size=391156k,mode=700,uid=1000,gid=1000)
fusectl on /sys/fs/fuse/connections type fusectl (rw,relatime)
gvfsd-fuse on /run/user/1000/gvfs type fuse.gvfsd-fuse (rw,nosuid,nodev,relatime,user_id=1000,group_id=1000)
[kirk@arch ~]$ df -T
Filesystem     Type     1K-blocks      Used Available Use% Mounted on
/dev/sda2      ext4      19097236  15345076   2759024  85% /
dev            devtmpfs   1952992         0   1952992   0% /dev
run            tmpfs      1955776       776   1955000   1% /run
tmpfs          tmpfs      1955776     19588   1936188   2% /dev/shm
tmpfs          tmpfs      1955776         0   1955776   0% /sys/fs/cgroup
tmpfs          tmpfs      1955776       840   1954936   1% /tmp
/dev/sda1      ext4        271811     35372    217887  14% /boot
/dev/sda4      ext4     364952052 248399124  97991384  72% /home
/dev/sda3      ext4      95993864  23493720  67600804  26% /srv
tmpfs          tmpfs       391156        16    391140   1% /run/user/1000
[kirk@arch ~]$ sudo blkid
/dev/sda1: UUID="89a7c749-1c9e-4563-a00e-121c6d5d3161" TYPE="ext4" PARTUUID="000cf18c-01" 
/dev/sda2: UUID="6e433e45-f41a-423a-96fe-28e05d3b458f" TYPE="ext4" PARTUUID="000cf18c-02" 
/dev/sda3: UUID="3db7ebaf-b1de-4711-ba04-326573f4f714" TYPE="ext4" PARTUUID="000cf18c-03" 
/dev/sda4: UUID="4e2ff47c-4c2c-4b33-929c-9364d317f39d" TYPE="ext4" PARTUUID="000cf18c-04" 
/dev/sdb1: UUID="fb6f5666-6075-4cfc-9105-30052be224e3" TYPE="ext4" PARTUUID="000cf18c-01" 
/dev/sdb2: UUID="92d68525-22b2-4619-a35a-0ba35df05b89" TYPE="ext4" PARTUUID="000cf18c-02" 
/dev/sdb3: UUID="35b3b21c-82f5-4db6-8406-8bd19c9d4aeb" TYPE="ext4" PARTUUID="000cf18c-03" 
/dev/sdb5: UUID="fcb00885-7ad0-46c0-8d68-40cde74e1a1a" TYPE="ext4" PARTUUID="000cf18c-05" 
[kirk@arch ~]$ sudo fdisk -l

Disk /dev/sda: 465.8 GiB, 500107862016 bytes, 976773168 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0x000cf18c

Device    Boot     Start       End    Blocks  Id System
/dev/sda1 *           63    578339    289138+ 83 Linux
/dev/sda2         578340  39648419  19535040  83 Linux
/dev/sda3       39648420 234966689  97659135  83 Linux
/dev/sda4      234966690 976773167 370903239  83 Linux


Disk /dev/sdb: 931.5 GiB, 1000204886016 bytes, 1953525168 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0x000cf18c

Device    Boot     Start        End    Blocks  Id System
/dev/sdb1 *           63     578339    289138+ 83 Linux
/dev/sdb2         578340   39648419  19535040  83 Linux
/dev/sdb3       39648420  470036479 215194030  83 Linux
/dev/sdb4      918548505 1360758783 221105139+  5 Extended
/dev/sdb5      918548568 1360754687 221103060  83 Linux

Tell me what else to run and I will. smile

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#9 2014-07-06 20:36:56

CaptainKirk
Member
Registered: 2009-06-07
Posts: 391

Re: My extra.db File is Haywire

This too:

$ sudo cat /proc/filesystems
nodev	sysfs
nodev	rootfs
nodev	ramfs
nodev	bdev
nodev	proc
nodev	cgroup
nodev	cpuset
nodev	tmpfs
nodev	devtmpfs
nodev	binfmt_misc
nodev	debugfs
nodev	securityfs
nodev	sockfs
nodev	pipefs
nodev	configfs
nodev	devpts
nodev	hugetlbfs
nodev	autofs
nodev	pstore
nodev	mqueue
	ext3
	ext2
	ext4
	fuseblk
nodev	fuse
nodev	fusectl

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#10 2014-07-09 11:44:23

CaptainKirk
Member
Registered: 2009-06-07
Posts: 391

Re: My extra.db File is Haywire

Any ideas here what to do? I'm sort of stuck.

Shall I boot from USB and mount this disk and remove this Device File?

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#11 2014-07-09 13:25:29

x33a
Forum Fellow
Registered: 2009-08-15
Posts: 4,587

Re: My extra.db File is Haywire

Try running fsck either through a live medium or

# touch /forcefsck

and reboot.

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#12 2014-07-09 14:46:25

CaptainKirk
Member
Registered: 2009-06-07
Posts: 391

Re: My extra.db File is Haywire

I tried that and also 

touch /etc/forcefsck

and reboot. fsck appears to run and says that /dev/sda2 1 3 4 are all clean. Running

sudo stat /var/lib/pacman/sync/extra.db

gives the same results however. sad

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#13 2014-07-09 17:20:08

x33a
Forum Fellow
Registered: 2009-08-15
Posts: 4,587

Re: My extra.db File is Haywire

Try running a SMART scan.

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#14 2014-07-09 20:54:47

CaptainKirk
Member
Registered: 2009-06-07
Posts: 391

Re: My extra.db File is Haywire

Here is what I got

[kirk@arch ~]$ lsblk
NAME   MAJ:MIN RM   SIZE RO TYPE MOUNTPOINT
sda      8:0    0 465.8G  0 disk 
├─sda1   8:1    0 282.4M  0 part /boot
├─sda2   8:2    0  18.6G  0 part /
├─sda3   8:3    0  93.1G  0 part /srv
└─sda4   8:4    0 353.7G  0 part /home
sdb      8:16   0 931.5G  0 disk 
├─sdb1   8:17   0 282.4M  0 part 
├─sdb2   8:18   0  18.6G  0 part 
├─sdb3   8:19   0 205.2G  0 part 
├─sdb4   8:20   0     1K  0 part 
└─sdb5   8:21   0 210.9G  0 part 
[kirk@arch ~]$ sudo smartctl -a /dev/sda2
smartctl 6.2 2013-07-26 r3841 [x86_64-linux-3.14.6-1-ARCH] (local build)
Copyright (C) 2002-13, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Family:     SAMSUNG SpinPoint F3
Device Model:     SAMSUNG HD502HJ
Serial Number:    S20BJ90B983233
LU WWN Device Id: 5 0024e9 206255b87
Firmware Version: 1AJ10001
User Capacity:    500,107,862,016 bytes [500 GB]
Sector Size:      512 bytes logical/physical
Rotation Rate:    7200 rpm
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   ATA8-ACS T13/1699-D revision 6
SATA Version is:  SATA 2.6, 3.0 Gb/s
Local Time is:    Wed Jul  9 23:52:44 2014 IDT
SMART support is: Available - device has SMART capability.
SMART support is: Enabled

=== START OF READ SMART DATA SECTION ===
SMART overall-health self-assessment test result: PASSED

General SMART Values:
Offline data collection status:  (0x00)	Offline data collection activity
					was never started.
					Auto Offline Data Collection: Disabled.
Self-test execution status:      (   0)	The previous self-test routine completed
					without error or no self-test has ever 
					been run.
Total time to complete Offline 
data collection: 		( 4800) seconds.
Offline data collection
capabilities: 			 (0x5b) SMART execute Offline immediate.
					Auto Offline data collection on/off support.
					Suspend Offline collection upon new
					command.
					Offline surface scan supported.
					Self-test supported.
					No Conveyance Self-test supported.
					Selective Self-test supported.
SMART capabilities:            (0x0003)	Saves SMART data before entering
					power-saving mode.
					Supports SMART auto save timer.
Error logging capability:        (0x01)	Error logging supported.
					General Purpose Logging supported.
Short self-test routine 
recommended polling time: 	 (   2) minutes.
Extended self-test routine
recommended polling time: 	 (  80) minutes.
SCT capabilities: 	       (0x003f)	SCT Status supported.
					SCT Error Recovery Control supported.
					SCT Feature Control supported.
					SCT Data Table supported.

SMART Attributes Data Structure revision number: 16
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED  WHEN_FAILED RAW_VALUE
  1 Raw_Read_Error_Rate     0x002f   100   100   051    Pre-fail  Always       -       8
  2 Throughput_Performance  0x0026   055   055   000    Old_age   Always       -       4395
  3 Spin_Up_Time            0x0023   083   082   025    Pre-fail  Always       -       5337
  4 Start_Stop_Count        0x0032   100   100   000    Old_age   Always       -       209
  5 Reallocated_Sector_Ct   0x0033   252   252   010    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x002e   252   252   051    Old_age   Always       -       0
  8 Seek_Time_Performance   0x0024   252   252   015    Old_age   Offline      -       0
  9 Power_On_Hours          0x0032   100   100   000    Old_age   Always       -       18015
 10 Spin_Retry_Count        0x0032   252   252   051    Old_age   Always       -       0
 11 Calibration_Retry_Count 0x0032   252   252   000    Old_age   Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       218
191 G-Sense_Error_Rate      0x0022   100   100   000    Old_age   Always       -       296
192 Power-Off_Retract_Count 0x0022   252   252   000    Old_age   Always       -       0
194 Temperature_Celsius     0x0002   064   061   000    Old_age   Always       -       33 (Min/Max 12/39)
195 Hardware_ECC_Recovered  0x003a   100   100   000    Old_age   Always       -       0
196 Reallocated_Event_Count 0x0032   252   252   000    Old_age   Always       -       0
197 Current_Pending_Sector  0x0032   252   252   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0030   252   252   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x0036   200   200   000    Old_age   Always       -       0
200 Multi_Zone_Error_Rate   0x002a   100   100   000    Old_age   Always       -       4
223 Load_Retry_Count        0x0032   252   252   000    Old_age   Always       -       0
225 Load_Cycle_Count        0x0032   100   100   000    Old_age   Always       -       218

SMART Error Log Version: 1
No Errors Logged

SMART Self-test log structure revision number 1
Num  Test_Description    Status                  Remaining  LifeTime(hours)  LBA_of_first_error
# 1  Extended offline    Completed without error       00%     18013         -
# 2  Extended offline    Completed without error       00%      5262         -
# 3  Short offline       Completed without error       00%      5261         -

SMART Selective self-test log data structure revision number 0
Note: revision number not 1 implies that no selective self-test has ever been run
 SPAN  MIN_LBA  MAX_LBA  CURRENT_TEST_STATUS
    1        0        0  Completed [00% left] (0-65535)
    2        0        0  Not_testing
    3        0        0  Not_testing
    4        0        0  Not_testing
    5        0        0  Not_testing
Selective self-test flags (0x0):
  After scanning selected spans, do NOT read-scan remainder of disk.
If Selective self-test is pending on power-up, resume after 0 minute delay.

I think it looks OK.

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#15 2014-07-09 21:50:59

Slithery
Administrator
From: Norfolk, UK
Registered: 2013-12-01
Posts: 5,776

Re: My extra.db File is Haywire

CaptainKirk wrote:

I think it looks OK.

Really? What about the several pre-fail results indicating your drive is on the verge of failing.

Make sure your backups are good and get a new drive ASAP would be my recommendation.

Last edited by Slithery (2014-07-09 21:52:44)

No, it didn't "fix" anything. It just shifted the brokeness one space to the right. - jasonwryan
Closing -- for deletion; Banning -- for muppetry. - jasonwryan

aur - dotfiles

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#16 2014-07-09 22:01:45

WorMzy
Forum Moderator
From: Scotland
Registered: 2010-06-16
Posts: 11,904
Website

Re: My extra.db File is Haywire

slithery wrote:
CaptainKirk wrote:

I think it looks OK.

Really? What about the several pre-fail results indicating your drive is on the verge of failing.

Make sure your backups are good and get a new drive ASAP would be my recommendation.

There were no pre-fails. The TYPE column indicates the severity of the failure if it has failed. The WHEN_FAILED column indicates whether it has failed or not.From 'man smartctl':

              If the Attribute's current Normalized value is less than or equal to the  threshold
              value,  then  the  "WHEN_FAILED" column will display "FAILING_NOW". If not, but the
              worst recorded value is less than or equal to the threshold value, then this column
              will display "In_the_past".  If the "WHEN_FAILED" column has no entry (indicated by
              a dash: '-') then this Attribute is OK now (not failing) and has also never  failed
              in the past.

I have been following this thread with interest, but have no constructive suggestions to make. I just wanted to voice that that smartctl output is perfectly fine, the problem appears to be strictly a filesystem one, not a hardware one.

Sakura:-
Mobo: MSI MAG X570S TORPEDO MAX // Processor: AMD Ryzen 9 5950X @4.9GHz // GFX: AMD Radeon RX 5700 XT // RAM: 32GB (4x 8GB) Corsair DDR4 (@ 3000MHz) // Storage: 1x 3TB HDD, 6x 1TB SSD, 2x 120GB SSD, 1x 275GB M2 SSD

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#17 2014-07-09 22:05:46

Slithery
Administrator
From: Norfolk, UK
Registered: 2013-12-01
Posts: 5,776

Re: My extra.db File is Haywire

WorMzy wrote:

There were no pre-fails. The TYPE column indicates the severity of the failure if it has failed. The WHEN_FAILED column indicates whether it has failed or not.

Sorry, my mistake. It's been years since I've used smart in any depth.

Last edited by Slithery (2014-07-09 22:06:34)

No, it didn't "fix" anything. It just shifted the brokeness one space to the right. - jasonwryan
Closing -- for deletion; Banning -- for muppetry. - jasonwryan

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#18 2014-07-10 05:47:53

x33a
Forum Fellow
Registered: 2009-08-15
Posts: 4,587

Re: My extra.db File is Haywire

The SMART output is indeed fine, but your drive has already run for 18000+ hours, which is quite a lot. You should keep backups handy, just in case wink

As for the problem, I am out of ideas for the possible reasons that could have caused it.

You can try removing the file using a live medium as you previously said.

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#19 2014-07-10 08:10:51

R00KIE
Forum Fellow
From: Between a computer and a chair
Registered: 2008-09-14
Posts: 4,734

Re: My extra.db File is Haywire

Wouldn't deleting/moving extra.db and then doing 'pacman -Sy' solve the problem?

R00KIE
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#20 2014-07-10 08:29:51

x33a
Forum Fellow
Registered: 2009-08-15
Posts: 4,587

Re: My extra.db File is Haywire

@ R00KIE, the OP is unable to delete the file when booted into the system. Read the first post.

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#21 2014-07-10 18:23:55

R00KIE
Forum Fellow
From: Between a computer and a chair
Registered: 2008-09-14
Posts: 4,734

Re: My extra.db File is Haywire

My bad, didn't read it properly. Then how about renaming/deleting the whole directory and creating and new one and 'pacman -Sy'?

I do agree that file looks really wonky, at a minimum I would backup everything and then manually force a fsck from a live medium, maybe even increasing the verbosity to see if you can get any clues as to what is happening.

If that doesn't get you anywhere the quickish way to solve it is to format the whole partition and copy everything back (who knows how that problem came to be and when/how it will case more trouble later).

R00KIE
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#22 2014-07-10 18:32:58

Trilby
Inspector Parrot
Registered: 2011-11-29
Posts: 29,568
Website

Re: My extra.db File is Haywire

Can you boot into a live media?  (or did I miss this already mentioned somewhere).

You can then mount that partition and explore a little better.  You could likely remove the file from the live system.  But better yet, you could investigate while that partition is not in use - so if it is a 'device' as it seems be treated, it may look different from the live system.  Or it might not be there at all from the live system if it is not really an on-disk file.  But this too would be worth knowing.

"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#23 2014-07-13 17:23:50

CaptainKirk
Member
Registered: 2009-06-07
Posts: 391

Re: My extra.db File is Haywire

R00KIE wrote:

My bad, didn't read it properly. Then how about renaming/deleting the whole directory and creating and new one and 'pacman -Sy'?

I don't think it's very smart to suggest to replace /var on a live system.

Wait a minute, maybe you meant just to replace /var/lib/pacman/sync/ . Now that's actually a VERY good (and very easy) idea. I did that and now ran pacman -Syu successfully and it created a new extra.db as it should be and I upgraded 352 packages (a record for me).

I did have to manually edit my mirrorlist to get a good, up-to-date mirror for a few packages, but anyhow, everything has been updated. smile

Thank you!

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#24 2014-07-13 17:30:38

karol
Archivist
Registered: 2009-05-06
Posts: 25,440

Re: My extra.db File is Haywire

You don't have to update the mirrorlist manually https://wiki.archlinux.org/index.php/Reflector

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#25 2014-07-13 18:16:39

R00KIE
Forum Fellow
From: Between a computer and a chair
Registered: 2008-09-14
Posts: 4,734

Re: My extra.db File is Haywire

CaptainKirk wrote:

I don't think it's very smart to suggest to replace /var on a live system.

Wait a minute, maybe you meant just to replace /var/lib/pacman/sync/ . Now that's actually a VERY good (and very easy) idea. I did that and now ran pacman -Syu successfully and it created a new extra.db as it should be and I upgraded 352 packages (a record for me).

Yes I meant renaming only /var/lib/pacman/sync smile

I guess you should still try to figure out what's going on with that weird db file though, it shouldn't happen so something may be wrong.

R00KIE
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